Abstract
Identification of chemically homologous microcrystals in a polycrystal sample is a big challenge and requires developing specific highly sensitive tools. Second harmonic (SHG) and coherent anti-Stokes Raman scattering (CARS) spectroscopy can be used to reveal arrangement of thymine molecules, one of the DNA bases, in microcrystalline sample. Strong dependence of CARS and SHG intensity on the orientation of the linear polarization of the excitation light allows to obtain high resolution images of thymine microcrystals by additionally utilizing the scanning microscopy technique. Experimental findings and theoretical interpretation of the results are compared. Presented experimental data together with quantum chemistry-based theoretical interpretation allowed us to determine the most probable organization of the thymine molecules.
Highlights
The nucleic acid bases—thymine (5-methyluracil), adenine, cytosine, uracil and guanine through hydrogen bonds and stacking interactions self-assemble into nanostructures of different dimensionality[1,2]
The second harmonic generation (SHG) is a second order non-linear optical process that occurs in the ordered materials with non-centrosymmetric structure and is sensitive to the macroscopic details of the self-assembly[17]
Thymine preparations on a glass coverslip were probed by a combination of the coherent anti-Stokes Raman scattering (CARS) and SHG microscopies
Summary
The nucleic acid bases—thymine (5-methyluracil), adenine, cytosine, uracil and guanine through hydrogen bonds and stacking interactions self-assemble into nanostructures of different dimensionality[1,2] While such structures are not found in Nature, detailed information on intermolecular forces which hold the DNA structure, becomes encoded in crystal forms, formation energies as well as in thermodynamic properties of the crystals[3,4,5]. The ordering of this self-arrangement depends on the type of substrate used for the assembly. While the techniques have long history in material research, the bulk nonlinear optical studies of thymine to date[24,25,26,27] were not able to distinguish the different polymorphs of thymine crystals
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